He was a historian at Tel Aviv University from the mid-1970s, serving as head of the School of History from 1982 to 1986. His initial field of study was Spanish history, and his 1983 biography of the former Spanish Dictator, General Primo de Rivera (1923–1930), is recognized as the most authoritative study on this subject. He later turned his attention to the history of Israel and the Middle East, leaving a legacy of expertise in Spanish inter-war year politics.

Ben-Ami remained Foreign Minister and Security Minister until March 2001, when, having won elections, Ariel Sharon took over from Barak. Ben-Ami refused to serve in the Sharon government and resigned from the Knesset in August 2002.

In their report published in 2003, the Or Commission held him responsible for the behavior of security forces during the October 2000 riots in which Israeli police killed 12 Israeli Arabs and one Palestinian, and failed to predict and control rioting which resulted in the death of a Jewish Israeli. The report recommended that Ben-Ami be disqualified from serving as Internal Security Minister in the future.[2] Despite the disqualification, Ben-Ami was not considered to be a hard-liner in Israeli relations with the Palestinians and during his time in the Barak government, he was a political rival of Shimon Peres.

Ben-Ami is currently Vice-President of the Toledo International Centre for Peace (TICpax), which, according to its mission statement, "seeks to contribute to the prevention and resolution of violent or potentially violent international or intranational conflicts and to the consolidation of peace, within a framework of respect and promotion of Human Rights and democratic values."